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Protein

ATP-dependent RNA helicase DBP6

Gene

DBP6

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

ATP-binding RNA helicase involved in the biogenesis of 60S ribosomal subunits and is required for the normal formation of 25S and 5.8S rRNAs.4 Publications

Catalytic activityi

ATP + H2O = ADP + phosphate.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi234 – 2418ATPPROSITE-ProRule annotation

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • ATP-dependent RNA helicase activity Source: SGD
  • RNA binding Source: UniProtKB-KW

GO - Biological processi

  • maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Source: SGD
  • maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Source: SGD
  • RNA secondary structure unwinding Source: GO_Central
Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase

Keywords - Biological processi

Ribosome biogenesis, rRNA processing

Keywords - Ligandi

ATP-binding, Nucleotide-binding, RNA-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-33348-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
ATP-dependent RNA helicase DBP6 (EC:3.6.4.13)
Alternative name(s):
DEAD box protein 6
Gene namesi
Name:DBP6
Ordered Locus Names:YNR038W
ORF Names:N3302
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XIV

Organism-specific databases

EuPathDBiFungiDB:YNR038W.
SGDiS000005321. DBP6.

Subcellular locationi

GO - Cellular componenti

  • nucleolus Source: SGD
  • preribosome, large subunit precursor Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 629629ATP-dependent RNA helicase DBP6PRO_0000055036Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei73 – 731PhosphoserineCombined sources
Modified residuei77 – 771PhosphoserineCombined sources
Modified residuei78 – 781PhosphoserineCombined sources

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP53734.
PRIDEiP53734.

PTM databases

iPTMnetiP53734.

Interactioni

Subunit structurei

Associated with pre-ribosomal particles. Interacts with DBP9 and RSA3. Together with NOP8, URB1, URB2 and RSA3, forms an RNA-independent complex, which is required during early maturation of nascent 60S ribosomal subunits.3 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
RSA3Q059423EBI-5625,EBI-33602
URB1P342414EBI-5625,EBI-26595
URB2P471084EBI-5625,EBI-25492

Protein-protein interaction databases

BioGridi35864. 31 interactions.
IntActiP53734. 43 interactions.
MINTiMINT-2731978.

Structurei

3D structure databases

ProteinModelPortaliP53734.
SMRiP53734. Positions 172-599.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini221 – 401181Helicase ATP-bindingPROSITE-ProRule annotationAdd
BLAST
Domaini437 – 603167Helicase C-terminalPROSITE-ProRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi197 – 2059Q motif
Motifi341 – 3444DEAD box

Domaini

The Q motif is unique to and characteristic of the DEAD box family of RNA helicases and controls ATP binding and hydrolysis.

Sequence similaritiesi

Contains 1 helicase ATP-binding domain.PROSITE-ProRule annotation
Contains 1 helicase C-terminal domain.PROSITE-ProRule annotation

Phylogenomic databases

GeneTreeiENSGT00550000075141.
HOGENOMiHOG000203294.
InParanoidiP53734.
KOiK14807.
OMAiSSQQYVH.
OrthoDBiEOG7HXD0B.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR011545. DEAD/DEAH_box_helicase_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR000629. RNA-helicase_DEAD-box_CS.
[Graphical view]
PfamiPF00270. DEAD. 1 hit.
PF00271. Helicase_C. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
PROSITEiPS00039. DEAD_ATP_HELICASE. 1 hit.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P53734-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MFASRFDPSQ LTAPAASAPE GIVGTTPPAI VPLKRQATES DNEEYGSHQD
60 70 80 90 100
SDESSNSSSE EDEDRMQVDY GASEEDSSEV EEEESKPSTH STVLSRFKQT
110 120 130 140 150
VSLQERLGAS DIAESKEDEG IEDEAASTHQ LKQIPQPEFV KNPMNLNTNS
160 170 180 190 200
LQFKSTGWLN TEKIYYDNSL IKPFSDYANE LEAKLLQNIC KNFSTNTFPI
210 220 230 240 250
QSIILDSILP VLNFTLNVSK RNFTRRIGDI LVNAATGSGK TLAYSIPIVQ
260 270 280 290 300
TLFKRQINRL RCIIIVPTKL LINQVYTTLT KLTQGTSLIV SIAKLENSLK
310 320 330 340 350
DEHKKLSNLE PDILITTPGR LVDHLNMKSI NLKNLKFLII DEADRLLNQS
360 370 380 390 400
FQGWCPKLMS HLKTDKLDTL PGNVIKMIFS ATLTTNTEKL NGLNLYKPKL
410 420 430 440 450
FLKQTDKLYQ LPNKLNEFNI NIPTAKSVYK PLILLYSICQ FMAHSPIAAK
460 470 480 490 500
ILIFVKSNES SIRLSKLLQL ICESRSQSSV LKNLQNLAVS INSVNSNNSK
510 520 530 540 550
AENKKIVANF SHHSESAGIT ILITTDIMSR GIDINDITQV INYDPPMSSQ
560 570 580 590 600
QYVHRVGRTA RANELGSAYN LLVGRGERTF FDDLNKDLDR DGKSVQPLEL
610 620
DFTLLESDSE LYTSSLESLK NYHNNTAQA
Length:629
Mass (Da):70,362
Last modified:October 1, 1996 - v1
Checksum:i64A04A2D88F44072
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z71653 Genomic DNA. Translation: CAA96318.1.
BK006947 Genomic DNA. Translation: DAA10580.1.
PIRiS63369.
RefSeqiNP_014436.1. NM_001183215.1.

Genome annotation databases

EnsemblFungiiYNR038W; YNR038W; YNR038W.
GeneIDi855774.
KEGGisce:YNR038W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z71653 Genomic DNA. Translation: CAA96318.1.
BK006947 Genomic DNA. Translation: DAA10580.1.
PIRiS63369.
RefSeqiNP_014436.1. NM_001183215.1.

3D structure databases

ProteinModelPortaliP53734.
SMRiP53734. Positions 172-599.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi35864. 31 interactions.
IntActiP53734. 43 interactions.
MINTiMINT-2731978.

PTM databases

iPTMnetiP53734.

Proteomic databases

MaxQBiP53734.
PRIDEiP53734.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYNR038W; YNR038W; YNR038W.
GeneIDi855774.
KEGGisce:YNR038W.

Organism-specific databases

EuPathDBiFungiDB:YNR038W.
SGDiS000005321. DBP6.

Phylogenomic databases

GeneTreeiENSGT00550000075141.
HOGENOMiHOG000203294.
InParanoidiP53734.
KOiK14807.
OMAiSSQQYVH.
OrthoDBiEOG7HXD0B.

Enzyme and pathway databases

BioCyciYEAST:G3O-33348-MONOMER.

Miscellaneous databases

PROiP53734.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR011545. DEAD/DEAH_box_helicase_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR000629. RNA-helicase_DEAD-box_CS.
[Graphical view]
PfamiPF00270. DEAD. 1 hit.
PF00271. Helicase_C. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
PROSITEiPS00039. DEAD_ATP_HELICASE. 1 hit.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its evolutionary implications."
    Philippsen P., Kleine K., Poehlmann R., Duesterhoeft A., Hamberg K., Hegemann J.H., Obermaier B., Urrestarazu L.A., Aert R., Albermann K., Altmann R., Andre B., Baladron V., Ballesta J.P.G., Becam A.-M., Beinhauer J.D., Boskovic J., Buitrago M.J.
    , Bussereau F., Coster F., Crouzet M., D'Angelo M., Dal Pero F., De Antoni A., del Rey F., Doignon F., Domdey H., Dubois E., Fiedler T.A., Fleig U., Floeth M., Fritz C., Gaillardin C., Garcia-Cantalejo J.M., Glansdorff N., Goffeau A., Gueldener U., Herbert C.J., Heumann K., Heuss-Neitzel D., Hilbert H., Hinni K., Iraqui Houssaini I., Jacquet M., Jimenez A., Jonniaux J.-L., Karpfinger-Hartl L., Lanfranchi G., Lepingle A., Levesque H., Lyck R., Maftahi M., Mallet L., Maurer C.T.C., Messenguy F., Mewes H.-W., Moestl D., Nasr F., Nicaud J.-M., Niedenthal R.K., Pandolfo D., Pierard A., Piravandi E., Planta R.J., Pohl T.M., Purnelle B., Rebischung C., Remacha M.A., Revuelta J.L., Rinke M., Saiz J.E., Sartorello F., Scherens B., Sen-Gupta M., Soler-Mira A., Urbanus J.H.M., Valle G., Van Dyck L., Verhasselt P., Vierendeels F., Vissers S., Voet M., Volckaert G., Wach A., Wambutt R., Wedler H., Zollner A., Hani J.
    Nature 387:93-98(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  2. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  3. "Dbp6p is an essential putative ATP-dependent RNA helicase required for 60S-ribosomal-subunit assembly in Saccharomyces cerevisiae."
    Kressler D., de la Cruz J., Rojo M., Linder P.
    Mol. Cell. Biol. 18:1855-1865(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION.
  4. "Synthetic lethality with conditional dbp6 alleles identifies Rsa1p, a nucleoplasmic protein involved in the assembly of 60S ribosomal subunits."
    Kressler D., Doere M., Rojo M., Linder P.
    Mol. Cell. Biol. 19:8633-8645(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  5. "Dbp9p, a putative ATP-dependent RNA helicase involved in 60S-ribosomal-subunit biogenesis, functionally interacts with Dbp6p."
    Daugeron M.-C., Kressler D., Linder P.
    RNA 7:1317-1334(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH DBP9.
  6. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  7. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  8. "The putative RNA helicase Dbp6p functionally interacts with Rpl3p, Nop8p and the novel trans-acting Factor Rsa3p during biogenesis of 60S ribosomal subunits in Saccharomyces cerevisiae."
    de la Cruz J., Lacombe T., Deloche O., Linder P., Kressler D.
    Genetics 166:1687-1699(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH RSA3, ASSOCIATION WITH PRE-RIBOSOMAL PARTICLES.
  9. "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae."
    Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P.
    J. Proteome Res. 6:1190-1197(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-73; SER-77 AND SER-78, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Strain: ADR376.
  10. "Characterization of Saccharomyces cerevisiae Npa2p (Urb2p) reveals a Low-molecular-mass complex containing Dbp6p, Npa1p (Urb1p), Nop8p, and Rsa3p involved in early steps of 60S ribosomal subunit biogenesis."
    Rosado I.V., Dez C., Lebaron S., Caizergues-Ferrer M., Henry Y., de la Cruz J.
    Mol. Cell. Biol. 27:1207-1221(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN A COMPLEX WITH NOP8; RSA3; URB1 AND URB2.
  11. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
    Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
    Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-73; SER-77 AND SER-78, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiDBP6_YEAST
AccessioniPrimary (citable) accession number: P53734
Secondary accession number(s): D6W1L4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: October 1, 1996
Last modified: July 6, 2016
This is version 144 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 12700 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  3. Yeast chromosome XIV
    Yeast (Saccharomyces cerevisiae) chromosome XIV: entries and gene names

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.